title: Potential roles of synonymous codon usage and tRNA concentration in hosts on the two initiation regions of foot-and-mouth disease virus RNA.
abstract: The open reading frame of foot-and-mouth disease virus (FMDV) contains two authentic initiation codons and the second initiation codon is often selected in high frequency. In the study, we analyzed the effects of the host-cell synonymous codon usage and the overall tRNA concentration in the hosts on the region flanked by the two initiation codons (termed as the region 1) and the same length starting from the second initiation codon (defined as the region 2). We find that low-usage codons of hosts are more selected in the region 1 than the region 2; no obvious usage bias of codon with high C/G content exists in the region 1, and the latter part (ranging from the 13th codon position to the 28th codon position) of the region 1 generally contains the codon sites with the generally lower tRNA concentration than the counterpart of the region 2. The low-usage codons of the hosts with high selection in the region 1 and the cluster codon position with low tRNA concentration in the region 1 may serve as potential factors in decreasing the translation rate of the region 1 caused by initiation from the first start codon of FMDV.
authors.affiliation: State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 Gansu, PR China.
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Zhou
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.forename: Dong-Jie
authors.initials: DJ
authors.lastname: Sun
authors.forename: Qi
authors.initials: Q
authors.lastname: Ma
authors.forename: Bing
authors.initials: B
authors.lastname: Ma
authors.forename: Zygmunt
authors.initials: Z
authors.lastname: Pejsak
authors.forename: Hao-Tai
authors.initials: HT
authors.lastname: Chen
authors.forename: Li-Na
authors.initials: LN
authors.lastname: Ma
authors.forename: Yao-Zhong
authors.initials: YZ
authors.lastname: Ding
authors.forename: Yong-Sheng
authors.initials: YS
authors.lastname: Liu
mesh_terms: D000818:Animals; D018387:Codon, Initiator; D029544:Foot-and-Mouth Disease Virus / Q000235:genetics*; D016366:Open Reading Frames; D014176:Protein Biosynthesis; D012343:RNA, Transfer / Q000378:metabolism*; D012367:RNA, Viral / Q000378:metabolism*
chemical_list: D018387:Codon, Initiator; D012367:RNA, Viral; D012343:RNA, Transfer
keywords: Foot-and-mouth disease virus; Gene expression; In-frame start codon; Low-usage codon; tRNA content